Variant report

Variant	rs788164
Chromosome Location	chr2:172913390-172913391
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:172912138..172914042-chr2:172960241..172963066,2	MCF-7	breast:
2	chr2:172908370..172912601-chr2:172912982..172915334,3	K562	blood:
3	chr2:172805225..172806853-chr2:172911394..172913520,2	K562	blood:
4	chr2:172909379..172916271-chr2:172947539..172952263,13	K562	blood:
5	chr2:172904276..172906441-chr2:172912588..172915159,2	K562	blood:
6	chr2:172903508..172905484-chr2:172912161..172915678,3	MCF-7	breast:
7	chr2:172911212..172913559-chr2:172957702..172960003,2	MCF-7	breast:
8	chr2:172901732..172906441-chr2:172911766..172917938,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000144355	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1008152	0.95[EUR][1000 genomes]
rs10167594	0.91[JPT][hapmap]
rs10171214	0.86[JPT][hapmap]
rs10203462	0.84[ASN][1000 genomes]
rs1038564	0.91[JPT][hapmap]
rs10497377	0.81[JPT][hapmap]
rs10930503	0.91[JPT][hapmap]
rs11885320	0.86[AFR][1000 genomes]
rs11892858	0.86[JPT][hapmap]
rs12328877	0.80[ASN][1000 genomes]
rs12616766	0.91[JPT][hapmap]
rs12622144	0.91[JPT][hapmap]
rs13403822	0.91[JPT][hapmap]
rs17428076	0.80[CEU][hapmap];0.83[TSI][hapmap]
rs17428174	0.85[CEU][hapmap]
rs17500114	0.84[CEU][hapmap];0.86[TSI][hapmap]
rs17581610	0.86[JPT][hapmap]
rs17615589	0.90[JPT][hapmap]
rs17615607	0.90[JPT][hapmap]
rs3796058	0.90[JPT][hapmap]
rs55791993	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62183852	0.93[EUR][1000 genomes]
rs6704590	0.85[CEU][hapmap]
rs6737876	0.93[EUR][1000 genomes]
rs6751078	0.86[JPT][hapmap]
rs6761111	0.85[CEU][hapmap]
rs705870	0.84[CEU][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs788161	1.00[CEU][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs788163	0.90[CEU][hapmap];0.86[MEX][hapmap]
rs788168	1.00[CEU][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1012188	chr2:172855923-172928891	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv875412	chr2:172903124-172942448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv583629	chr2:172907898-172914293	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs788164	BBS5	cis	cerebellum	SCAN
rs788164	SLC25A12	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172907800-172916000	Weak transcription	Fetal Kidney	kidney
2	chr2:172911000-172930000	Weak transcription	Primary T cells from cord blood	blood
3	chr2:172911200-172915600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:172911200-172947200	Weak transcription	HSMM	muscle
5	chr2:172911400-172914400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:172911400-172915200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:172911400-172916400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:172911400-172916600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:172911400-172916800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr2:172911600-172913400	Enhancers	HepG2	liver
11	chr2:172911800-172913400	Enhancers	K562	blood
12	chr2:172912200-172916400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:172912200-172917000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:172912600-172913400	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr2:172912800-172913400	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr2:172913000-172917000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:172913200-172917000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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